Ok I am not an engineer, well ok I am , but not with Anodized materials , but something did cross my mind.
I looked up how Anodizing is done. If you look at how the iphone is engineered you can see that white flakes of aluminium are flying off as the tool rounds the device. These are under a lot of friction and heat and are most likely "Sticking" to the device as the tool does it's job. The white flakes are flying off as you can see in the video and some of them DO settle back onto the device.
Look here : Time: 04:55 - you can see white flakes sticking to the actual device.
http://www.youtube.com/watch?v=TLCvajE7sgM
What chemicals will attack an anodize? High heat may be an issue. When tools which rotate at certain high speeds touch a device it causes friction and heat.
That might be a possibility but that's what QC is for. To discard those phones which got any kind of defect!